[English] 日本語
Yorodumi
- PDB-9iit: Full length structure of FKP in complex with GTP and GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iit
TitleFull length structure of FKP in complex with GTP and GDP
ComponentsL-fucokinase/L-fucose-1-P guanylyltransferase
KeywordsTRANSFERASE / fucose / ATP / GTP / kinase / pyrophosphorylase
Function / homology
Function and homology information


fucokinase / fucose-1-phosphate guanylyltransferase / fucokinase activity / GDP-L-fucose salvage / nucleotidyltransferase activity / ATP binding
Similarity search - Function
L-fucokinase / Fucose pyrophosphorylase domain / : / Galactokinase/homoserine kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / MALONIC ACID / L-fucokinase/L-fucose-1-P guanylyltransferase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKo, T.P. / Lin, S.W. / Hsu, M.F. / Lin, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural insight into the catalytic mechanism of the bifunctional enzyme l-fucokinase/GDP-fucose pyrophosphorylase.
Authors: Lin, S.W. / Ko, T.P. / Chiang, H.Y. / Wu, C.G. / Hsu, M.F. / Wang, A.H. / Lin, C.H.
History
DepositionJun 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-fucokinase/L-fucose-1-P guanylyltransferase
B: L-fucokinase/L-fucose-1-P guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,60415
Polymers215,9082
Non-polymers2,69513
Water15,187843
1
A: L-fucokinase/L-fucose-1-P guanylyltransferase
B: L-fucokinase/L-fucose-1-P guanylyltransferase
hetero molecules

A: L-fucokinase/L-fucose-1-P guanylyltransferase
B: L-fucokinase/L-fucose-1-P guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,20730
Polymers431,8174
Non-polymers5,39126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area20910 Å2
ΔGint-65 kcal/mol
Surface area140820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.821, 96.061, 127.369
Angle α, β, γ (deg.)90.000, 97.094, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISSERSER(chain 'A' and resid 0 through 1001)AA0 - 94920 - 969
12GTPGTPGTPGTP(chain 'A' and resid 0 through 1001)AC1001
23HISHISSERSER(chain 'B' and resid 0 through 1001)BB0 - 94920 - 969
24GTPGTPGTPGTP(chain 'B' and resid 0 through 1001)BJ1001

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein L-fucokinase/L-fucose-1-P guanylyltransferase


Mass: 107954.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: fkp / Plasmid: pET16b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q58T34

-
Non-polymers , 7 types, 856 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 8% Tascimate, 20% PEG 3350, 15mM GTP, 15mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 111983 / % possible obs: 98.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 42.37 Å2 / CC1/2: 0.918 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11074 / CC1/2: 0.696 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 6LH3 and 6LH5

6lh3
PDB Unreleased entry

6lh5
PDB Unreleased entry


Resolution: 2.3→29.15 Å / SU ML: 0.3196 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.093
RfactorNum. reflection% reflection
Rfree0.2315 1968 1.79 %
Rwork0.1999 --
obs0.2005 110219 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15038 0 45 843 15926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002215433
X-RAY DIFFRACTIONf_angle_d0.549820942
X-RAY DIFFRACTIONf_chiral_restr0.0422290
X-RAY DIFFRACTIONf_plane_restr0.00412680
X-RAY DIFFRACTIONf_dihedral_angle_d15.15739213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.35041330.3127436X-RAY DIFFRACTION94
2.36-2.420.29931410.2697753X-RAY DIFFRACTION98.7
2.42-2.490.32621410.29077708X-RAY DIFFRACTION98.44
2.49-2.570.36611280.31457085X-RAY DIFFRACTION90.08
2.57-2.660.28751420.24917827X-RAY DIFFRACTION99.5
2.66-2.770.26181430.2417886X-RAY DIFFRACTION99.95
2.77-2.90.30081410.25757758X-RAY DIFFRACTION98.38
2.9-3.050.30481430.23147847X-RAY DIFFRACTION99.95
3.05-3.240.28961420.24687743X-RAY DIFFRACTION97.9
3.24-3.490.25671420.20537808X-RAY DIFFRACTION99.28
3.49-3.840.21791440.18317878X-RAY DIFFRACTION99.39
3.84-4.40.17691400.15667662X-RAY DIFFRACTION96.69
4.4-5.530.17441430.14547916X-RAY DIFFRACTION99.33
5.53-29.150.17691450.16537944X-RAY DIFFRACTION98.29
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.68334070052-0.743523170888-0.0326297090571.711247882510.1025673546181.127367232950.3408952095650.5538361007190.0831758265596-0.589374483009-0.0374225599749-0.725103259560.0652363156920.836627253559-0.2322127501960.9626324575730.1317058146440.008085699128420.913981846015-0.1056009272730.70513783618770.852952033375.44663245463.420283142
20.979015292217-0.487814898097-0.2671451215941.387929757320.5310809164031.721998087130.2908378322160.131915212163-0.249854095634-0.3181315262480.214744528935-0.3395424275520.7214732581490.550525055426-0.4102889741490.7380370860950.0606428830922-0.1773712734810.46155963038-0.0389244552420.51903738948561.269010212974.27117868677.938837839
32.5050534779-0.0798588653070.365285517992.07325480070.3167609463181.580814237140.1804732204780.116546246415-0.027623468811-0.231146148482-0.0147034332579-0.2016538796391.08384119720.0146502151962-0.05299135761971.446712269930.169408880252-0.2368632045230.696462282434-0.115040388280.65602438590364.57363809255.199931548173.6694029413
40.7213157924090.1729359304640.301113064741.22200438927-0.4456306606370.621092276337-0.06476426153850.362428286016-0.0770154452074-0.2552429187770.312376873877-0.4020071591750.5367852889030.861520519302-0.1420344855631.512017237080.234735351927-0.4407784733130.928826093526-0.2247422043180.89097041025164.969996196555.948510671273.1810981676
51.80939896253-0.3220627751270.7086788185450.2027086785890.2542821838592.493470172640.203860469251-0.2753742889460.104108771919-0.4011289411190.1508082438320.2246739095520.890051873343-0.575401742445-0.2073651993320.697512118047-0.21629782334-0.1176304909070.5809336599840.1564410053150.55695577254746.705591105677.380933144989.258260335
62.18050047619-0.6014344452571.066516158632.0959489434-0.1820569030112.253650524910.166008353047-0.270001286127-0.129533166114-0.5026832699320.009855641721290.3342414468320.363398016179-0.63270670564-0.1282428561450.651989421284-0.140035513074-0.2164793094030.5312820021070.1232819678760.51592091544438.479615189883.334797446271.0053217613
71.88390448961-0.103257084063-0.6298772909280.8443766671410.2249859538372.343191776581.141380593630.786511326267-0.336764822881-0.897232450436-0.2235231116260.6015228075730.725094778125-0.6487314496471.476728741541.47238106057-0.253006783996-0.8644387905970.6237846989450.06124843353140.47528782417634.914015394874.55274288355.3031609124
81.14834310663-0.8939650668240.3492803043681.72515454030.8395288285421.898543216190.0192232492190.1131555207810.12215055257-0.4475254317950.1312181604260.00133924985087-0.1028083608580.0279686119271-0.1209686116260.684615588839-0.0794782500245-0.1244682892350.3833560751950.1103531844970.41447393749549.885883420989.355240587770.155043668
94.117158831080.04994210018421.214501274582.973020954330.1913626037363.24937273045-0.87966650687-0.828047042370.981772188481-0.04368729940150.383483770011-0.151591767235-0.730567453898-0.221439039340.3204698450020.574684817210.110946823093-0.1982187248460.52646058955-0.07990041826430.61063640772959.2609406648100.19049814592.9215837628
101.06605445152-0.06325819812610.2555236723711.283662121510.3959982472321.11554847902-0.0367353353673-0.128990774868-0.03049777746180.0540719671305-0.009721797317820.04822364845870.119044370682-0.1253927083550.06969476273530.2054053131620.007982373813510.04236809862120.2483274606820.01764625409360.26193470830177.450291254488.0674658905119.103855871
111.83960292353-0.167489747877-0.3396278325411.193974194790.01553756359541.86645504161-0.0321435092431-0.2287721703920.2324418140710.01302895363830.0155930542820.290594038542-0.270291851582-0.1223538237160.04162793556460.2220102744410.03210262717930.01197858405360.26187643504-0.03038364720050.32973912330475.6181488613104.002554957125.478726342
120.3736655554490.08132530410980.6151503143251.155669881380.7201882347721.5115407149-0.0593191542075-0.02792025370940.030305921944-0.0720250379629-0.09469527277970.3253306711670.0962170742801-0.3040036910470.1115655858940.253162080768-0.01984779432130.02946691379620.283001153566-0.02315228825040.35679066089972.240256175886.2616113738115.739126878
132.40792195515-0.005268889558360.4584237282390.1235456676130.227221062461.0296783406-0.1299677685920.1440599816630.123165503099-0.2514894461770.00113837013942-0.1872495843960.00285089465820.09140033968910.11512730360.352052836457-0.04005554328750.0173387876760.274972935079-0.01412471732330.31835768282379.229075689979.0405816971100.355160974
142.501017453760.3871970956030.08418806193990.823595457705-0.1439129858361.79936693018-0.1212664838360.421905304941-0.121693571239-0.3540248683110.132015819288-0.26258237006-0.06266784689910.330964505746-0.01843458469940.392612296706-0.02602987818060.08763997674520.408965145744-0.04308814769880.31870279073690.410028937877.609916551997.2083438556
151.596130147650.219775405993-0.8859645460061.429956264230.9909018313331.75709564527-0.3535788453260.0653185131601-0.02872081822490.01750205375730.272470197578-0.04088554044690.2703437578210.1940890120370.115328894780.2581480231420.005120955500130.01321908894880.3317878569510.03055473671180.31499076051391.17547201682.9415496543114.799298105
162.51273881958-0.0920867548151-0.9257108380863.070103835491.241133912881.78037358727-0.0868947444690.0185880755064-0.01955595076010.5327058492290.05258057768360.1731726993470.251910094435-0.04351222682920.05787729408970.458408785578-0.1279084950990.02583710298130.5279240768270.03547690054930.40473090617427.493235187657.3189285593121.430901514
171.34274796512-0.39045049268-0.7317244268742.13742087380.6831745119861.507818072570.1700287253530.2472561994190.22008826336-0.0895991804044-0.230087246897-0.28501525239-0.12693963491-0.08475944269590.1055264096540.341174974943-0.05582703646520.03585108768660.5086337854240.08987267353310.44337966992937.21907321757.4675460957107.301515531
181.452650381610.195216913898-0.8226180140232.509878039360.007927110320122.550070934230.1183008519130.1377187275280.6341423855660.0870867547352-0.055858234092-0.0728544881004-0.4352306809740.057713884029-0.07606166993350.399357680839-0.0874804259610.02766340269390.4797781132650.1073578795150.71884029754434.440964288977.6408006348111.299519427
191.502341372150.228039461928-0.07666822129141.32675084816-1.213524159841.156039599720.346590704521-0.08238514337740.8016692738310.253386528791-0.2454924446-0.0283419754193-0.438956586983-0.02326945708680.002347212519080.49540996731-0.09219561221380.08448173306730.4817068070360.04941903403910.8524115156334.227342635776.681349915111.897716509
203.9668841537-0.646554098479-1.043137493091.386262481050.7237534766531.37825180706-0.1149209052581.01121152991-0.244185792013-0.3813057661140.0251753371979-0.5758789673140.2630949056390.325549725507-0.03606255357470.920972204345-0.02310106930560.2057205458791.101523996150.07428071085170.64298410998743.381400720853.362122585591.0209935585
212.06797262687-0.001992455801810.4951744861892.564184804760.8991052432541.968636468770.09872297246940.686336619138-0.223086023095-0.599828551663-0.3248086910560.4413430955570.169598751461-0.6289250345450.1449635224020.595900476229-0.065792774264-0.06629433121550.993962938964-0.1363066203670.49211965398923.177568480145.577703837989.5012031947
222.133967143760.0197205744781-0.1040589944611.818149442870.1602964255141.96031669149-0.2078985588030.7387604467560.242418276761-0.594854000424-0.152533167140.783359716553-0.232396714367-1.161653270830.296722542510.643532270274-0.0394381404841-0.119712896311.517697984-0.09308830725970.8527594630066.4892291684853.253072908890.978941464
232.30255556687-1.24142011727-0.44923111011.582039267420.3967703079381.185220692160.2187111352560.305615519343-0.102951268571-0.0136865617892-0.4181938950090.4188596274840.20170341953-0.5252338013270.06937067235330.436873889801-0.167097785453-0.01795843591760.7268661262-0.1979415322250.64765327191626.937257263241.1278823157100.92343983
244.155806664160.08710083462460.3518803319782.352334501710.2955957950152.971064586820.2817994566750.376080977198-0.7818254425090.2949915815290.140664174351-0.3741428524320.8752704665570.445686728946-0.2952893980220.664444983087-0.00104044011865-0.09845605035240.528720008047-0.1838795610030.71812139950452.070052171831.8116866614102.923761112
251.56457868655-0.655297515646-0.1184159609881.747678217630.6030882013950.936923459689-0.09328381549670.1356732649310.09936586140060.03523947918750.0666760314393-0.03809493309030.08377611432940.1087093229440.02644251728980.308510266023-0.03996945316580.06473095698060.277417718125-0.01907169631020.40354599494180.69461642744.0136626844114.958183692
261.74710061710.2496581521280.5464911806811.807651428630.2176982784672.354974058650.00296849581830.256027172602-0.417380442114-0.137641222770.0715901178046-0.08012804079510.3732199017080.188525962338-0.1112667315080.3350946052390.05534795701430.01621853909240.282691052865-0.07945279216990.41506144905686.51485598227.9046156798112.111383219
271.53919510911-1.154073207040.5723861006841.2695389337-0.04237104147940.6654506964490.1485544147770.227793185501-0.0578639718274-0.31458669725-0.137794972690.05796100419920.09661086714670.00874395916541-0.005099528603390.302911305179-0.01230594053180.03542054389490.273176001612-0.0004394281196820.4599224608876.357265913445.7571792354110.476665269
281.94792080428-0.3186173411671.022605592460.4555157339330.1199344452242.257328933740.124387428094-0.177082781219-0.2770946360410.204281872142-0.02583158264370.1293134774280.236786910685-0.179200575084-0.08052295369310.294429407422-0.02205577957630.05531179763810.2694671606220.008203219913720.43531882357563.31520282353.1960907553120.173922578
292.70944335144-0.09069384506980.8758093244781.395905411820.1006438165462.36691008888-0.117799448344-0.88009700344-0.3360503688370.392624450840.1438602744040.1558552379070.111848563168-0.362036745449-0.003585193048710.3536547307490.02299073273210.1222599987410.4853074951860.0720488993860.48080997782261.884161863954.3329637619131.804162653
302.16130217475-1.09782405321-0.3387249225021.831703953870.5073162922862.766911318750.0942343724134-0.535250374384-0.06901730676720.1174326107910.254960998489-0.167258706628-0.0765199824572-0.0244618933975-0.2986824787890.358148764135-0.0540402395984-0.01538414709890.4325153682880.04422612391990.52553278897579.279913084248.881771133128.906828235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 275 )
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 305 )
6X-RAY DIFFRACTION6chain 'A' and (resid 306 through 380 )
7X-RAY DIFFRACTION7chain 'A' and (resid 381 through 460 )
8X-RAY DIFFRACTION8chain 'A' and (resid 461 through 495 )
9X-RAY DIFFRACTION9chain 'A' and (resid 496 through 570 )
10X-RAY DIFFRACTION10chain 'A' and (resid 571 through 635 )
11X-RAY DIFFRACTION11chain 'A' and (resid 636 through 710 )
12X-RAY DIFFRACTION12chain 'A' and (resid 711 through 790 )
13X-RAY DIFFRACTION13chain 'A' and (resid 791 through 855 )
14X-RAY DIFFRACTION14chain 'A' and (resid 856 through 925 )
15X-RAY DIFFRACTION15chain 'A' and (resid 926 through 949 )
16X-RAY DIFFRACTION16chain 'B' and (resid 0 through 75 )
17X-RAY DIFFRACTION17chain 'B' and (resid 76 through 145 )
18X-RAY DIFFRACTION18chain 'B' and (resid 146 through 235 )
19X-RAY DIFFRACTION19chain 'B' and (resid 236 through 275 )
20X-RAY DIFFRACTION20chain 'B' and (resid 276 through 305 )
21X-RAY DIFFRACTION21chain 'B' and (resid 306 through 380 )
22X-RAY DIFFRACTION22chain 'B' and (resid 381 through 460 )
23X-RAY DIFFRACTION23chain 'B' and (resid 461 through 495 )
24X-RAY DIFFRACTION24chain 'B' and (resid 496 through 570 )
25X-RAY DIFFRACTION25chain 'B' and (resid 571 through 635 )
26X-RAY DIFFRACTION26chain 'B' and (resid 636 through 710 )
27X-RAY DIFFRACTION27chain 'B' and (resid 711 through 790 )
28X-RAY DIFFRACTION28chain 'B' and (resid 791 through 855 )
29X-RAY DIFFRACTION29chain 'B' and (resid 856 through 925 )
30X-RAY DIFFRACTION30chain 'B' and (resid 926 through 949 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more